Introduction: Free living amoebas are opportunistic pathogens that usually exist in different environmental conditions such as warm and polluted water, even in water supply networks and they could cause serious diseases in humans. So, due to their medical importance, identification of free living amoeba in water resources is necessary. Materials and Methods: Water samples were collected from 70 water wells, 30 water resources and 20 water supply networks in the first six months of 2010. Then, the samples were cultured on non-nutrient agar and the amoeba were collected and stained by Giemsa stain for morphological studies. Results: 42 out of 120 samples (35%) contained free living amoeba. Out of them, 31 samples (73.81%) were polluted with one amoeba and 11 (26.19%) with one amoeba. The frequency of Acanthamoeba species (39 cases) was higher than that of Neagleria (14 cases) and the wells were more polluted than others (44.40%). Based on morphological characteristics, four pathogenic ameba were identified (Naegleria fowleri, Acanthamoeba polyphaga, A.castellani and A.astronyxis). Conclusions: The results showed that water resources contained free living amoeba and some important and pathogenic species of these amoebas were identified by morphological characteristics. Thus, it is necessary to employ new methods for disinfection and filtration of water resources so that the infection with free living amoeba and infectious agents is prevented.